Recent human fMRI and monkey electrophysiology has shown that MT neurons are tuned to 3D direction. Furthermore, both psychophysics and single-unit recordings in MT have demonstrated that 3D motion signals arise from two distinct binocular cues: changing disparity (CD), and inter-ocular velocity differences (IOVD). We assessed how these two binocular cues for 3D motion interact in the visual hierarchy using an fMRI adaptation paradigm. We tested (1) whether CD- and IOVD-isolating stimuli could generate 3D direction-selective adaptation using cue-congruent test stimuli, and (2) whether cross-cue adaptation occurred. In a fully-crossed design, the adapter was either an IOVD or CD stimulus, and the test probe was either an IOVD or CD stimulus (or a “Full” cue stimulus containing both CD and IOVD). On a given scan, observers were adapted to either towards or away 3D motion of one adapting cue (e.g., IOVD towards) and tested with all possible combinations of test stimulus (CD, IOVD, and Full) and motion direction (towards/away). We found robust adaptation effects for cue-congruent conditions: after adaptation to IOVD and testing with IOVD, or after adaptation to CD and testing with CD, the fMRI response in MT+ was lower when the test direction was the same as the adapting direction compared to when the test direction was the opposite. However, we found no adaptation in MT+ in cross-cue conditions: IOVD adaptation did not affect CD test responses in a direction-selective manner, and vice versa. In V1 there was no adaptation effect across all conditions, consistent with previous findings suggesting that 3D motion signals are computed after V1. The lack of cross-cue interactions in MT+ suggests that, even though both CD and IOVD stimuli drive MT neurons, they represent distinct channels of 3D motion information.